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annotate summarize_taxa.xml @ 0:c1bd0c560018 draft default tip

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author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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c1bd0c560018 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
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1 <tool id="qiime_summarize_taxa" name="Summarize taxa" version="1.9.1">
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2 <description>and store results in a new table or appended to an existing
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3 mapping file
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4 </description>
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5
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9
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10 <expand macro="requirements" />
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11
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12 <version_command><![CDATA[
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13 summarize_taxa.py --version
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14 ]]>
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15 </version_command>
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17 <command>
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18 <![CDATA[
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19 summarize_taxa.py
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20 -i $otu_table_fp
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21 -o summarize_taxa
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22
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23 -L $level
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24
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25 #if str($mapping) != 'None':
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26 -m $mapping
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27 #end if
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28
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29 --md_identifier $md_identifier
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30
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31 $md_as_string
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32
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33 $absolute_abundance
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34
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35 #if str( $lower_percentage )
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36 -l $lower_percentage
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37 #end if
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38
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39 #if str( $upper_percentage)
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40 -u $upper_percentage
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41 #end if
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42
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43 $transposed_output
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44 $suppress_classic_table_output
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45 $suppress_biom_table_output
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46 ]]>
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47 </command>
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48
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49 <inputs>
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50 <param name="otu_table_fp" type="data" format="tabular,tsv,txt,biom"
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51 label="Input OTU table" help="(-i/--otu_table_fp)"/>
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52
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53 <param name="level" type="select" label="Taxonomic level to summarize by"
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54 help="(-L/--level)" multiple="True" display="checkboxes">
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55 <option value="1" >Kingdom</option>
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56 <option value="2" selected="true">Phylum</option>
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57 <option value="3" selected="true">Class</option>
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58 <option value="4" selected="true">Order</option>
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59 <option value="5" selected="true">Family</option>
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60 <option value="6" selected="true">Genus</option>
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61 <option value="7" >Species</option>
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62 </param>
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63
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64 <param name="mapping" type="data" format="tabular,tsv,csv"
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65 label="Input metadata mapping (optional)" help="If supplied, then the
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66 taxon information will be added to this file. This option is useful for
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67 coloring PCoA plots by taxon abundance or to perform statistical
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68 tests of taxon/mapping associations (-m/--mapping)" optional="True"/>
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69
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70 <param name="md_identifier" type="text" value="taxonomy" label="Relevant
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71 observation metadata key" help="(--md_identifier)" />
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72
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73 <param name="md_as_string" type="boolean" label="Include metadata as string?"
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74 truevalue="--md_as_string" falsevalue="" checked="False"
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75 help="By default, metadata is included as list (--md_as_string)" />
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76
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77 <param name="absolute_abundance" type="boolean" label="Report absolute
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78 abundance?" truevalue="--absolute_abundance" falsevalue="" checked="False"
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79 help="By default, relative abundance is reported (--absolute_abundance)" />
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80
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81 <param name="lower_percentage" type="float" label="Percentage threshold to
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82 remove highly present OTU (optional)" help="If present, OTUs having
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83 higher absolute abundance are trimmed. To remove OTUs that make up
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84 more than 5% of the total dataset you would pass 0.05 (-l/--lower_percentage)"
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85 optional="True"/>
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86
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87 <param name="upper_percentage" type="float" label="Percentage threshold to
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88 remove lowly present OTU (optional)" help="If present, OTUs having
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89 lower absolute abundance are trimmed. To remove the OTUs that
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90 makes up less than 45% of the total dataset you would pass 0.45
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91 (-u/--upper_percentage)" optional="True"/>
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92
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93 <param name="transposed_output" type="boolean" label="Transpose output?"
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94 truevalue="--transposed_output" falsevalue="" checked="False"
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95 help="If checked, the output will be written transposed from the
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96 regular output. This is helpful in cases when you want to use Site
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97 Painter to visualize your data (-t/--transposed_output)" />
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98
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99 <param name="suppress_classic_table_output" type="boolean"
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100 label="Suppress creation of the classic (TSV) format taxon table?"
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101 truevalue="--suppress_classic_table_output" falsevalue="" checked="False"
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102 help="This option is ignored if a mapping file is present
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103 (--suppress_classic_table_output)" />
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104
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105 <param name="suppress_biom_table_output" type="boolean"
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106 label="Suppress creation of the BIOM-formatted taxon table?"
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107 truevalue="--suppress_biom_table_output" falsevalue="" checked="False"
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108 help="This option is ignored if a mapping file is present
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109 (--suppress_biom_table_output)" />
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110 </inputs>
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111
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112 <outputs>
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113 <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt"
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114 label="${tool.name} on ${on_string}: L1 tab">
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115 <filter>"1" in level and suppress_classic_table_output is False</filter>
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116 </data>
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117
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118 <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt"
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119 label="${tool.name} on ${on_string}: L2 tab">
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120 <filter>"2" in level and suppress_classic_table_output is False</filter>
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121 </data>
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122
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123 <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt"
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124 label="${tool.name} on ${on_string}: L3 tab">
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125 <filter>"3" in level and suppress_classic_table_output is False</filter>
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126 </data>
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127
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128 <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt"
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129 label="${tool.name} on ${on_string}: L4 tab">
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130 <filter>"4" in level and suppress_classic_table_output is False</filter>
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131 </data>
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132
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133 <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt"
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134 label="${tool.name} on ${on_string}: L5 tab">
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135 <filter>"5" in level and suppress_classic_table_output is False</filter>
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136 </data>
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137
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138 <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt"
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139 label="${tool.name} on ${on_string}: L6 tab">
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140 <filter>"6" in level and suppress_classic_table_output is False</filter>
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141 </data>
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142
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143 <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt"
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144 label="${tool.name} on ${on_string}: L7 tab">
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145 <filter>"7" in level and suppress_classic_table_output is False</filter>
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146 </data>
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147 </outputs>
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148
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149 <tests>
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150 <test>
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151 <param name="otu_table_fp"
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152 value="pick_open_reference_otus_otu_table_with_taxo.biom"/>
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153 <param name="level" value="2,3,4,5,6" />
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154 <param name="mapping"
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155 value="validate_mapping_file_corrected_map.tabular"/>
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156 <param name="md_identifier" value="taxonomy"/>
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157 <param name="md_as_string" value=""/>
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158 <param name="delimiter" value=";" />
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159 <param name="absolute_abundance" value=""/>
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160 <param name="transposed_output" value=""/>
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161 <param name="suppress_classic_table_output" value="" />
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162 <param name="suppress_biom_table_output" value="" />
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163
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164 <output name="L2_tab" value="summarize_taxa_L2.tabular" />
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165 <output name="L3_tab" value="summarize_taxa_L3.tabular" />
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166 <output name="L4_tab" value="summarize_taxa_L4.tabular" />
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167 <output name="L5_tab" value="summarize_taxa_L5.tabular" />
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168 <output name="L6_tab" value="summarize_taxa_L6.tabular" />
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169 </test>
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170 </tests>
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171
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172 <help><![CDATA[
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173
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174 **What it does**
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175
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176 This tool provides summary information of the representation of taxonomic groups within each sample. It takes an OTU table that contains taxonomic information as input.
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177
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178 More information about this tool is available on
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179 `QIIME documentation <http://qiime.org/scripts/summarize_taxa.html>`_.
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180 ]]>
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181 </help>
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182
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183 <citations>
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184 <expand macro="citations" />
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185 </citations>
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186 </tool>